GWAS Results

This analysis can be used to identify quantitative trait locus (QTL) by displaying associations between markers and traits for trials within the T3 database.
Analysis Methods: The analysis includes genotype and phenotype trials where there were more than 50 germplasm lines in common.
1. Trial Analysis - GWAS with no fixed effects.
2. Breeding Program Analysis - GWAS on a set of related phenotype trials (different location and same year or same location different year). Principle Components that accounted for more than 5% of the relationship matrix variance were included as fixed effects in the analysis. Each phenotype trial (if more than one) was included as a fixed effect.
GWAS: The analysis use rrBLUP GWAS package (Endleman, Jeffery, "Ridge Regression and Other Kernels for Genomic Selection with R package rrBLUP", The Plant Genome Vol 4 no. 3). The settings are: MAF > 0.05, P3D = TRUE (equivalent to EMMAX). The q-value is an estimate of significance given p-values from multiple comparisons using a false discovery rate of 0.05.
The z-value = qnorm( 1.0 - ( pvalue / 2.0 ))

Analysis Method: trial
breeding program